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- EMDB-9608: Anthrax Toxin Receptor 1-bound full particles of Seneca Valley Vi... -

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Basic information

Entry
Database: EMDB / ID: EMD-9608
TitleAnthrax Toxin Receptor 1-bound full particles of Seneca Valley Virus in acidic conditions
Map data
Sample
  • Virus: Seneca valley virus
    • Protein or peptide: VP1
    • Protein or peptide: VP3
    • Protein or peptide: VP2
    • Protein or peptide: VP4
    • Protein or peptide: Anthrax toxin receptor 1
  • Ligand: MAGNESIUM ION
KeywordsSeneca Valley virus / VIRUS
Function / homology
Function and homology information


reproductive process / filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / lamellipodium membrane / Uptake and function of anthrax toxins / collagen binding / substrate adhesion-dependent cell spreading / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...reproductive process / filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / lamellipodium membrane / Uptake and function of anthrax toxins / collagen binding / substrate adhesion-dependent cell spreading / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / actin filament binding / transmembrane signaling receptor activity / channel activity / actin cytoskeleton organization / monoatomic ion transmembrane transport / RNA helicase activity / endosome membrane / symbiont entry into host cell / external side of plasma membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / cell surface / proteolysis / RNA binding / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Picornavirus coat protein ...Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Picornavirus coat protein / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Anthrax toxin receptor 1
Similarity search - Component
Biological speciesSeneca valley virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLou ZY / Cao L
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Seneca Valley virus attachment and uncoating mediated by its receptor anthrax toxin receptor 1.
Authors: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li ...Authors: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li / Elizabeth E Fry / David I Stuart / Ping Qian / Zhiyong Lou / Zihe Rao /
Abstract: Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. SVV mediates cell entry by attachment to the receptor anthrax toxin receptor 1 (ANTXR1). Here ...Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. SVV mediates cell entry by attachment to the receptor anthrax toxin receptor 1 (ANTXR1). Here we determine atomic structures of mature SVV particles alone and in complex with ANTXR1 in both neutral and acidic conditions, as well as empty "spent" particles in complex with ANTXR1 in acidic conditions by cryoelectron microscopy. SVV engages ANTXR1 mainly by the VP2 DF and VP1 CD loops, leading to structural changes in the VP1 GH loop and VP3 GH loop, which attenuate interprotomer interactions and destabilize the capsid assembly. Despite lying on the edge of the attachment site, VP2 D146 interacts with the metal ion in ANTXR1 and is required for cell entry. Though the individual substitution of most interacting residues abolishes receptor binding and virus propagation, a serine-to-alanine mutation at VP2 S177 significantly increases SVV proliferation. Acidification of the SVV-ANTXR1 complex results in a major reconfiguration of the pentameric capsid assemblies, which rotate ∼20° around the icosahedral fivefold axes to form a previously uncharacterized spent particle resembling a potential uncoating intermediate with remarkable perforations at both two- and threefold axes. These structures provide high-resolution snapshots of SVV entry, highlighting opportunities for anticancer therapeutic optimization.
History
DepositionAug 1, 2018-
Header (metadata) releaseFeb 6, 2019-
Map releaseFeb 6, 2019-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6adm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9608.png

Downloads & links

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Map

FileDownload / File: emd_9608.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 550 pix.
= 599.5 Å		1.09 Å/pix.
x 550 pix.
= 599.5 Å		1.09 Å/pix.
x 550 pix.
= 599.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.0569943 - 0.12408534
Average (Standard dev.)0.00106498 (±0.006466932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions550550550
Spacing550550550
CellA=B=C: 599.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z550550550
origin x/y/z0.0000.0000.000
length x/y/z599.500599.500599.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-6-10-25
NX/NY/NZ564636
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS550550550
D min/max/mean-0.0570.1240.001

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Supplemental data

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Sample components

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Entire : Seneca valley virus

EntireName: Seneca valley virus
Components
  • Virus: Seneca valley virus
    • Protein or peptide: VP1
    • Protein or peptide: VP3
    • Protein or peptide: VP2
    • Protein or peptide: VP4
    • Protein or peptide: Anthrax toxin receptor 1
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Seneca valley virus

SupramoleculeName: Seneca valley virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 390157 / Sci species name: Seneca valley virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Seneca valley virus
Molecular weightTheoretical: 28.459969 KDa
SequenceString: STDNAETGVI EAGNTDTDFS GELAAPGSNH TNVKFLFDRS RLLNVIKVLE KDAVFPRPFP TQEGAQQDDG YFCLLTPRPT VASRPATRF GLYANPSGSG VLANTSLDFN FYSLACFTYF RSDLEVTVVS LEPDLEFAVG WFPSGSEYQA SSFVYDQLHV P FHFTGRTP ...String:
STDNAETGVI EAGNTDTDFS GELAAPGSNH TNVKFLFDRS RLLNVIKVLE KDAVFPRPFP TQEGAQQDDG YFCLLTPRPT VASRPATRF GLYANPSGSG VLANTSLDFN FYSLACFTYF RSDLEVTVVS LEPDLEFAVG WFPSGSEYQA SSFVYDQLHV P FHFTGRTP RAFASKGGKV SFVLPWNSVS SVLPVRWGGA SKLSSATRGL PAHADWGTIY AFVPRPNEKK STAVKHVAVY IR YKNARAW CPSMLPFRSY K

UniProtKB: Genome polyprotein

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Macromolecule #2: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Seneca valley virus
Molecular weightTheoretical: 26.296883 KDa
SequenceString: PIPTAPRENS LMFLSTLPDD TVPAYGNVRT PPVNYLPGEI TDLLQLARIP TLMAFERVPE PVPASDTYVP YVAVPTQFDD RPLISFPIT LSDPVYQNTL VGAISSNFAN YRGCIQITLT FCGPMMARGK FLLSYSPPNG TQPQTLSEAM QCTYSIWDIG L NSSWTFVV ...String:
PIPTAPRENS LMFLSTLPDD TVPAYGNVRT PPVNYLPGEI TDLLQLARIP TLMAFERVPE PVPASDTYVP YVAVPTQFDD RPLISFPIT LSDPVYQNTL VGAISSNFAN YRGCIQITLT FCGPMMARGK FLLSYSPPNG TQPQTLSEAM QCTYSIWDIG L NSSWTFVV PYISPSDYRE TRAITNSVYS ADGWFSLHKL TKITLPPDCP QSPCILFFAS AGEDYTLRLP VDCNPSYVF

UniProtKB: Genome polyprotein

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Macromolecule #3: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Seneca valley virus
Molecular weightTheoretical: 29.813266 KDa
SequenceString: DRVTTQTAGN TAINTQSSLG VLCAYVEDPT KSDPPSSSTD QPTTTFTAID RWYTGRLNSW TKAVKTFSFQ AVPLPGAFLS RQGGLNGGA FTATLHRHFL MKCGWQVQVQ CNLTQFHQGA LLVAMVPETT LDVKPDGKAK SLQELNEEQW VEMSDDYRTG K NMPFQSLG ...String:
DRVTTQTAGN TAINTQSSLG VLCAYVEDPT KSDPPSSSTD QPTTTFTAID RWYTGRLNSW TKAVKTFSFQ AVPLPGAFLS RQGGLNGGA FTATLHRHFL MKCGWQVQVQ CNLTQFHQGA LLVAMVPETT LDVKPDGKAK SLQELNEEQW VEMSDDYRTG K NMPFQSLG TYYRPPNWTW GPNFINPYQV TVFPHQILNA RTSTSVDINV PYIGETPTQS SETQNSWTLL VMVLVPLDYK EG ATTDPEI TFSVRPTSPY FNGLRNRYTA

UniProtKB: Genome polyprotein

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Seneca valley virus
Molecular weightTheoretical: 5.998467 KDa
SequenceString:
RGNNGNMTFN YYANTYQNSV DFSTSSSASG AGPGNSRGGL AGLLTNFSGI LNPLGYLK

UniProtKB: Genome polyprotein

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Macromolecule #5: Anthrax toxin receptor 1

MacromoleculeName: Anthrax toxin receptor 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.31602 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
SMACYGGFDL YFILDKSGSV LHHWNEIYYF VEQLAHKFIS PQLRMSFIVF STRGTTLMKL TEDREQIRQG LEELQKVLPG GDTYMHEGF ERASEQIYYE NRQGYRTASV IIALTDGELH EDLFFYSERE ANRSRDLGAI VYAVGVKDFN ETQLARIADS K DHVFPVND GFQALQGIIH SILKKSC

UniProtKB: Anthrax toxin receptor 1

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.63 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9167
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6adm:
Anthrax Toxin Receptor 1-bound full particles of Seneca Valley Virus in acidic conditions

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